DOCSLIB.ORG

Diverse Populations of Lake Water Bacteria Exhibit Chemotaxis Towards Inorganic Nutrients

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Diverse Populations of Lake Water Bacteria Exhibit Chemotaxis Towards Inorganic Nutrients The ISME Journal (2013) 7, 1661–1664 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej SHORT COMMUNICATION Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients Paul G Dennis1,2, Justin Seymour3, Kimber Kumbun2 and Gene W Tyson1,2 1Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia; 2Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia and 3Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, New South Wales, Australia Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes. The ISME Journal (2013) 7, 1661–1664; doi:10.1038/ismej.2013.47; published online 21 March 2013 Subject Category: Microbial population and community ecology Keywords: chemotaxis; microbial communities; 16S rRNA gene; inorganic substrates In aquatic environments, organic and inorganic sulphur compounds (Miller et al., 2004). In contrast, nutrients are distributed heterogeneously, with chemotaxis towards inorganic substrates is poorly microscale hotspots found throughout the water characterised despite bacterial growth in aquatic column (Azam, 1998; Blackburn et al., 1998). Micro- ecosystems often being limited by dissolved inor- bial cells are generally unable to uptake nutrients ganic nutrients (Church, 2008), and the requirement that are more than a few cell diameters away; for some inorganic chemicals in anaerobic respira- therefore, motility is a key determinant of the size tion (Thauer et al., 1977). In addition, as chemotaxis of the microhabitats within which different popula- studies have focussed on single populations of tions perceive and exploit nutrient sources (Stocker, cultivated bacteria, the generality of this trait is 2012). Non-motile cells can explore B80 nl water unknown. To date, chemotaxis towards inorganic per day, which when compared with ca. 1 ml per substrates has been observed towards: (1) ammo- day for motile cells is very small (Stocker, 2012). nium and nitrate by the marine cyanobacterium, Furthermore, as motility is typically associated with Synechococcus (Willey and Waterbury, 1989); (2) the ability of cells to sense and direct movement ammonium by the purple non-sulphur photosyn- along chemical gradients (chemotaxis), many motile thetic bacterium Rhodobacter sphaeroides (Ingham populations are not only able to explore large and Armitage, 1987; Poole and Armitage, 1989); (3) volumes of water, but are also able to move directly nitrate and nitrite by Shewanella putrefaciens towards perceived resource hotspots (Fenchel, 2002; (Nealson et al., 1995) and several strains of deni- Stocker et al., 2008; Stocker and Seymour, 2012). trifying bacteria (Kennedy and Lawless, 1985; Lee Aquatic bacterial chemotaxis occurs in response et al., 2002) and (4) phosphate by a heterotrophic to a wide range of organic substrates, including marine Thalassospira sp. (Hu¨ tz et al., 2011). amino acids (Barbara and Mitchell, 2003), sugars In this study, we used a syringe-based assay (Malmcrona-Friberg et al., 1990) and organic (Supplementary Figure S1), inspired by the tradi- tional capillary assay (Adler and Dahl, 1967), coupled with flow cytometry and 16S rRNA gene amplicon Correspondence: G Tyson, Australian Centre for Ecogenomics and pyrosequencing to enumerate and identify popula- Advanced Water Management Centre, School of Chemistry and tions within a lake water microbial community that Molecular Biosciences, The University of Queensland, Brisbane, exhibited chemotaxis towards ammonium, nitrate Queensland 4072, Australia. E-mail: [email protected] and phosphate. Chemotaxis assays were performed Received 16 October 2012; revised 11 February 2013; accepted 12 by submerging 1-ml syringes containing 80 mlof0.1M February 2013; published online 21 March 2013 chemoattractant (nitrate/ammonium/phosphate) into Bacterial chemotaxis towards inorganic nutrients PG Dennis et al 1662 lake water for 30 min (Supplementary information). Each chemoattractant was prepared in 0.2 mm- Circle size equals filtered lake water to ensure that the chemical cell count 0 2.5 k Ammonium Nitrate Control Lake water characteristics of the background solution in the Phosphate Bacteroidetes; Sphingobacteriales 1 syringe was similar to that in the lake. Filtered lake Sphingobacteria; water control assays with no added chemoattractant Sphingobacteriales Sphingobacteriales 2 were performed in parallel and facilitated the Sphingobacteriales 3 measurement of stochastic movement of cells into Pedobacter our assays (Supplementary Figure S2). All assays Betaproteobacteria; Comamonadaceae were replicated six times, providing three samples Burkholderiales Variovorax for cell counting and three samples that were pooled Burkholderiales for 16S rRNA gene amplicon sequencing. This novel Polynucleobacter approach facilitated culture-independent character- Methylophilales Methylophilaceae isation of chemotactic populations within a lake Gammaproteobacteria Sinobacteraceae water community. To ensure that counts in the Enterobacteriaceae assays reflected chemotaxis rather than growth OP3 OP3 stimulation, we enumerated cells in 0.2 mm-filtered Verrucomicrobia Verrucomicrobiales Actinobacteria; ACK-M1 1 lake water with and without added nutrients. The Actinomycetales controls were incubated for 30 min, but the tips of ACK-M1 2 the syringes were not submerged in lake water Cyanobacteria Dolichospermum Cyanobacteria 1 (Supplementary Figure S3). Cyanobacteria 2 Cell counts in the nutrient-spiked chemotaxis assays were approximately six times higher than in the control assays (Po0.001, generalized linear Figure 1 Bacterial operational taxonomic units (OTUs) present model; Supplementary Figures S2 and S3), but did at 41% abundance in any sample. The size of each circle not differ from one another. Cell counts in nutrient represents the relative abundance of each OTU normalised by the stimulation assays, however, did not differ from total cell count within each sample. The OTUs are organised by those associated with the filtered lake water control phylogenetic relatedness based on a maximum likelihood boot- (Supplementary Figure S3). These results indicate strapped tree (1000 iterations) of full-length sequences that were identified as the nearest BLAST matches for each OTU. Bootstrap that nitrate, ammonium and phosphate elicited values are represented as follows: 75–100% (closed circles), 50– strong chemotactic responses from at least one 74% (open circles), o50% (no circle). The compositional population within the lake water community and similarity of each community is represented at the base of the that slight differences in the diffusion coefficients of heatmap by a complete-linkage cluster analysis tree of OTU the attractants (ca. 0.17, 0.18 and 0.05 Â 104 cm2 s À 1 abundances. À þ 3 À for NO3 ,NH4 and PO4 , respectively) did not lead to differences in the strength of response. Three members of the Sphingobacteriales exhib- 0.6 ited the strongest chemotactic response to nitrate Control and phosphate (Figures 1 and 2). Phylogenetic 0.4 analysis (Supplementary information) revealed that these Sphingobacteriales populations belonged to Nitrate the family Chitophagaceae. Within this family, 0.2 members of the genera Niastella and Chitinophaga Sphingobacteriales 3 Sphingobacteriales 1 are known to exhibit gliding motility (Lim et al., 0 Phosphate 2009; Weon et al., 2009; Del Rio et al., 2010), and Methylophilaceae ACK-M1 1 Sphingobacteriales 2 some Chitinophaga species are known to reduce PC2 (11.4%) -0.2 nitrate as a terminal electron acceptor (Lim et al., Variovorax 2009). Interestingly, the only other Sphingobacter- iales population observed in the lake water at 41% -0.4 relative abundance, a Pedobacter-like organism, did not exhibit chemotaxis towards nitrate (Figure 1). -0.6 Ammonium This is consistent with observations that Pedobacter isolates do not reduce nitrate (Steyn et al., 1998). Therefore, the positive chemotactic response -0.50 0.5 towards nitrate observed for the Sphingobacteriales PC1 (88.0%) populations may reflect their ability to detect and Figure 2 PCA ordination highlighting differences in operational exploit nitrate as an alternative electron acceptor. taxonomic units (OTU) abundance between the chemotaxis Chemoattraction may also reflect the ability for cells assays. OTU abundances were calculated by normalising the relative abundances of each OTU by the total cell count within to move towards nitrate in response to inorganic each sample. The OTUs are
Load more

Recommended publications
  • Community Analysis of Microbial Sharing and Specialization in A
    Downloaded from http://rspb.royalsocietypublishing.org/ on March 15, 2017 Community analysis of microbial sharing rspb.royalsocietypublishing.org and specialization in a Costa Rican ant–plant–hemipteran symbiosis Elizabeth G. Pringle1,2 and Corrie S. Moreau3 Research 1Department of Biology, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Cite this article: Pringle EG, Moreau CS. 2017 Reno, NV 89557, USA 2Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA Community analysis of microbial sharing and 3Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, specialization in a Costa Rican ant–plant– Chicago, IL 60605, USA hemipteran symbiosis. Proc. R. Soc. B 284: EGP, 0000-0002-4398-9272 20162770. http://dx.doi.org/10.1098/rspb.2016.2770 Ants have long been renowned for their intimate mutualisms with tropho- bionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of Received: 14 December 2016 microbes between interacting macroorganisms, affects the composition and Accepted: 17 January 2017 function of symbiotic microbial communities. Here we approached this ques- tion by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and Subject Category: quantitative PCR to examine community structure of both bacteria and Ecology fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feed- ing scale insects and honeydew-feeding ants make use of microbial Subject Areas: symbionts to subsist on phloem-derived diets of suboptimal nutritional qual- ecology, evolution, microbiology ity.
    [Show full text]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Anti-Staphylococcal Activity of Variovorax Paradoxus EPS
    California State University, San Bernardino CSUSB ScholarWorks Electronic Theses, Projects, and Dissertations Office of aduateGr Studies 9-2017 Anti-Staphylococcal Activity of Variovorax paradoxus EPS Patricia Holt-Torres Follow this and additional works at: https://scholarworks.lib.csusb.edu/etd Part of the Other Microbiology Commons Recommended Citation Holt-Torres, Patricia, "Anti-Staphylococcal Activity of Variovorax paradoxus EPS" (2017). Electronic Theses, Projects, and Dissertations. 584. https://scholarworks.lib.csusb.edu/etd/584 This Thesis is brought to you for free and open access by the Office of aduateGr Studies at CSUSB ScholarWorks. It has been accepted for inclusion in Electronic Theses, Projects, and Dissertations by an authorized administrator of CSUSB ScholarWorks. For more information, please contact [email protected]. 0 Anti-Staphylococcal Activity of Variovorax paradoxus EPS A Thesis Presented to the Faculty of California State University, San Bernardino In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology by Patricia S. Holt-Torres September 2017 1 2 Table of Contents Page number Introduction 4 Evolution of Antibiotics and Antibiotic Resistance 4 in environmental and soil bacteria Antibiotic Classes and Mechanisms 4 Antimicrobial Resistance 6 Methicillin-Resistant Staphylococcus aureus (MRSA) 8 Novel antibiotics 10 Non-ribosomal peptide synthetases 10 Variovorax paradoxus EPS 11 Hypothesis 13 Methods and materials 14 Media and Culture Conditions 14 T-streak method to determine anti-staphylococcal activity 14 RNA extraction of Wild Type V. paradoxus EPS 15 Reverse Transcription of Wild type V. paradoxus EPS 16 Expression analysis of anti-staphylococcal activity of 16 Variovorax paradoxus EPS Quantitative analysis of anti-staphylococcal activity 17 Embedded S.
    [Show full text]
  • Table S1. Bacterial Otus from 16S Rrna
    Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria
    [Show full text]
  • Leadbetterella Byssophila Type Strain (4M15)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Leadbetterella byssophila type strain (4M15). Permalink https://escholarship.org/uc/item/907989cw Journal Standards in genomic sciences, 4(1) ISSN 1944-3277 Authors Abt, Birte Teshima, Hazuki Lucas, Susan et al. Publication Date 2011-03-04 DOI 10.4056/sigs.1413518 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:2-12 DOI:10.4056/sigs.1413518 Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Birte Abt1, Hazuki Teshima2,3, Susan Lucas2, Alla Lapidus2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Amrita Pati2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Brian J. Tindall1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk1, and Nikos C. Kyrpides2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Lawrence Livermore National Laboratory, Livermore, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C.
    [Show full text]
  • Multilevel Social Structure and Diet Shape the Gut Microbiota of the Gelada Monkey, the Only Grazing Primate Pål Trosvik 1*, Eric J
    Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate Pål Trosvik 1*, Eric J. de Muinck 1, Eli K. Rueness 1, Peter J. Fashing 2, Evan C. Beierschmitt 3, Kadie R. Callingham 4, Jacob B. Kraus 5, Thomas H. Trew 6, Amera Moges 7, Addisu Mekonnen 1,8 , Vivek V. Venkataraman 9, Nga Nguyen 2 Supplementary information: Supplementary Figures 1-17, Supplementary Tables 1-10. Figure S1. Relative abundances of the eight most prevalent phyla in the gelada samples. Data are shown for all samples combined, as well as split into samples collected during the dry or wet season. The category “Other” includes OTUs that could not be classified to the phylum level with a probability higher than 0.5. Figure S2. Between-sample weighted (a) and unweighted (b) UniFrac distances in gelada samples collected during the dry (n=142) or the wet (n=174) season. Each box represents the interquartile range, with the horizontal lines representing the medians and the whiskers representing 1.5 times the interquartile range. Points outside the whiskers represent outliers. For both comparisons the difference in mean distance was highly significant (t<<0.001 for both comparisons, unpaired t-tests). Figure S3. Non-metric multidimensional scaling of all primate samples based on weighted (a) and unweighted (b) UniFrac distances. The plot shows the two main dimensions of variation, with plotted characters color coded according to sample type. Clustering according to samples type was highly significant, explaining 46.2% and 63.1% of between-sample variation, respectively (p<<0.001 for both tests, PERMANOVA).
    [Show full text]
  • Pedobacter Ghigonii Sp. Nov., Isolated from the Microbiota of the Planarian Schmidtea Mediterranea
    Article Pedobacter ghigonii sp. nov., Isolated from the Microbiota of the Planarian Schmidtea mediterranea Luis Johnson Kangale 1,2 , Didier Raoult 2,3,4 and Fournier Pierre-Edouard 1,2,* 1 UMR VITROME, SSA, Aix-Marseille University, IRD, AP-HM, IHU-Méditerranée-Infection, 13385 Marseille, France; [email protected] 2 IHU-Méditerranée-Infection, 13385 Marseille, France; [email protected] 3 Department of Epidemiology of Parasitic Diseases, Aix Marseille University, IRD, AP-HM, MEPHI, 13385 Marseille, France 4 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia * Correspondence: [email protected]; Tel.: +33-0413732401; Fax: +33-0413732402 Abstract: The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investi- gated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with Citation: Kangale, L.J.; Raoult, D.; other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and Pierre-Edouard, F.
    [Show full text]
  • Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
    Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively).
    [Show full text]
  • Lifestyle Preferences Drive the Structure and Diversity of Bacterial and Archaeal Communities in a Small Riverine Reservoir
    www.nature.com/scientificreports OPEN Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir Carles Borrego1,2, Sergi Sabater1,3* & Lorenzo Proia1,4 Spatial heterogeneity along river networks is interrupted by dams, afecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil diferences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Diferences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir. Spatial heterogeneity of river networks results from the sequence of lotic segments—which promote the transport and quick transformation of materials—and lentic segments such as large pools and wetlands—which mostly contribute to the process and storage of organic matter 1,2.
    [Show full text]
  • University of California Riverside
    UNIVERSITY OF CALIFORNIA RIVERSIDE Selective Association Between the Free-Living Nematode Acrobeloides maximus and Soil Bacteria A Thesis submitted in partial satisfaction of the requirements for the degree of Master of Science in Genetics, Genomics and Bioinformatics by Sammy Farid Sedky June 2013 Thesis Committee: Dr. Paul De Ley, Chairperson Dr. Paul Orwin Dr. David Crowley Copyright by Sammy Farid Sedky 2013 The Thesis of Sammy Farid Sedky is approved: Committee Chairperson University of California, Riverside ACKNOWLEDGMENTS This master thesis would not have been possible without the help of several individuals who contributed their time, assistance, and expertise to the completion of this work: • To my advisor, Dr. Paul De Ley: Thank you for giving me a lab I could call home, where I was welcome and where I could grow as a researcher and scholar. Your assistance in navigating the labyrinth of challenges involved in the writing and completion of this document has been invaluable. Thank you for your guidance and support. • To Dr. Paul Orwin: I will always be grateful for the kind tutelage you provided during your sabbatical stay at UCR. This study could not have been completed without your vigilance. • To Dr. David Crowley: Thank you for allowing us to use Science Lab I 308 to perform most of the wet lab work and for your assistance as a committee member in the review and editing of this thesis. • To my colleagues, Dr. JP Baquiran and Brian Thater: It was a blast working with you both. Thanks for the laughs and good times. iv UCR DEDICATIONS • To my friend and protégé, Rosalynn Duong: I could not have chosen a better undergraduate assistant.
    [Show full text]
  • Lysine and Novel Hydroxylysine Lipids in Soil Bacteria: Amino Acid Membrane Lipid Response to Temperature and Ph in Pseudopedobacter Saltans
    Rowan University Rowan Digital Works School of Earth & Environment Faculty Scholarship School of Earth & Environment 6-1-2015 Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans Elisha Moore Rowan University Ellen Hopmans W. Irene Rijpstra Irene Sanchez Andrea Laura Villanueva See next page for additional authors Follow this and additional works at: https://rdw.rowan.edu/see_facpub Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Moore, E.K., Hopmans, E., Rijpstra, W.I.C., Sanchez-Andrea, I., Villanueva, L., Wienk, H., ...& Sinninghe Damste, J. (2015). Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Frontiers in Microbiology, Volume 6, Article 637. This Article is brought to you for free and open access by the School of Earth & Environment at Rowan Digital Works. It has been accepted for inclusion in School of Earth & Environment Faculty Scholarship by an authorized administrator of Rowan Digital Works. Authors Elisha Moore, Ellen Hopmans, W. Irene Rijpstra, Irene Sanchez Andrea, Laura Villanueva, Hans Wienk, Frans Schoutsen, Alfons Stams, and Jaap Sinninghe Damsté This article is available at Rowan Digital Works: https://rdw.rowan.edu/see_facpub/17 ORIGINAL RESEARCH published: 29 June 2015 doi: 10.3389/fmicb.2015.00637 Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans Eli K. Moore 1*, Ellen C. Hopmans 1, W. Irene C. Rijpstra 1, Irene Sánchez-Andrea 2, Laura Villanueva 1, Hans Wienk 3, Frans Schoutsen 4, Alfons J.
    [Show full text]
  • Bacteria Associated with Vascular Wilt of Poplar
    Bacteria associated with vascular wilt of poplar Hanna Kwasna ( [email protected] ) Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu https://orcid.org/0000-0001- 6135-4126 Wojciech Szewczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Marlena Baranowska Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Jolanta Behnke-Borowczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Research Article Keywords: Bacteria, Pathogens, Plantation, Poplar hybrids, Vascular wilt Posted Date: May 27th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-250846/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract In 2017, the 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. Leaves appeared smaller, turned yellow-brown, and were shed prematurely. Twigs and smaller branches died. Bark was sunken and discolored, often loosened and split. Trunks decayed from the base. Phloem and xylem showed brown necrosis. Ten per cent of trees died in 1–2 months. None of these symptoms was typical for known poplar diseases. Bacteria in soil and the necrotic base of poplar trunk were analysed with Illumina sequencing. Soil and wood were colonized by at least 615 and 249 taxa. The majority of bacteria were common to soil and wood. The most common taxa in soil were: Acidobacteria (14.757%), Actinobacteria (14.583%), Proteobacteria (36.872) with Betaproteobacteria (6.516%), Burkholderiales (6.102%), Comamonadaceae (2.786%), and Verrucomicrobia (5.307%).The most common taxa in wood were: Bacteroidetes (22.722%) including Chryseobacterium (5.074%), Flavobacteriales (10.873%), Sphingobacteriales (9.396%) with Pedobacter cryoconitis (7.306%), Proteobacteria (73.785%) with Enterobacteriales (33.247%) including Serratia (15.303%) and Sodalis (6.524%), Pseudomonadales (9.829%) including Pseudomonas (9.017%), Rhizobiales (6.826%), Sphingomonadales (5.646%), and Xanthomonadales (11.194%).
    [Show full text]